Place racks in upper and lower thirds of oven; preheat to 325°. Lightly coat edges of cups and tops of 3 standard 6-cup muffin pans with nonstick spray and line with paper liners. Sift almond flour through a fine-mesh sieve into a medium bowl; discard any large pieces. Whisk in baking powder and ¼ tsp. salt.

Using a stand mixer fitted with a whisk attachment, whisk eggs and granulated sugar on medium-high speed until pale and fluffy, about 5 minutes. Reduce speed to low and whisk in almond-flour mixture and 2 tsp. vanilla until smooth, about 1 minute. Divide batter among muffin cups. Bake cupcakes, rotating pans top to bottom halfway through, until a tester inserted into the centers comes out clean, 15–20 minutes. Transfer cupcakes to a wire rack and let cool.